4C77 | pdb_00004c77

Phenylacetone monooxygenase: oxidised R337K mutant in complex with APADP

• PDB DOI: https://doi.org/10.2210/pdb4C77/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermobifida fusca
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2013-09-19 Released: 2014-02-05 
• Deposition Author(s): Martinoli, C., Fraaije, M.W., Mattevi, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Beyond the Protein Matrix: Probing Cofactor Variants in a Baeyer-Villiger Oxygenation Reaction.

Martinoli, C., Dudek, H.M., Orru, R., Edmondson, D.E., Fraaije, M.W., Mattevi, A.

(2013) ACS Catal 3: 3058

• PubMed: 24443704 
• DOI: https://doi.org/10.1021/cs400837z
• Primary Citation Related Structures: 
  4C74, 4C77, 4OVI


• PubMed Abstract: 
  

  A general question in biochemistry is the interplay between the chemical properties of cofactors and the surrounding protein matrix. Here, the functions of NADP ⁺ and FAD are explored by investigation of a representative monooxygenase reconstituted with chemically-modified cofactor analogues. Like pieces of a jigsaw puzzle, the enzyme active site juxtaposes the flavin and nicotinamide rings, harnessing their H-bonding and steric properties to finely construct an oxygen-reacting center that restrains the flavin-peroxide intermediate in a catalytically-competent orientation. Strikingly, the regio- and stereoselectivities of the reaction are essentially unaffected by cofactor modifications. These observations indicate a remarkable robustness of this complex multi-cofactor active site, which has implications for enzyme design based on cofactor engineering approaches.

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Organizational Affiliation: 
• Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy.
Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
Departments of Biochemistry and Chemistry, Emory University, 1510 Clifton Road, Atlanta, GA 30322, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.97 kDa 
• Atom Count: 4,410 
• Modeled Residue Count: 531 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHENYLACETONE MONOOXYGENASE	A	542	Thermobifida fusca	Mutation(s): 1  EC: 1.14.13.92
UniProt
Find proteins for Q47PU3 (Thermobifida fusca (strain YX)) Explore Q47PU3  Go to UniProtKB:  Q47PU3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
N01	C [auth A]	3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE C22 H26 N6 O17 P3 CWZSJEPJRFQEBR-RBEMOOQDSA-K
P6G	D [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.36	α = 90
b = 107.36	β = 90
c = 106.79	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-05 
Deposition Author(s): Martinoli, C., Fraaije, M.W., Mattevi, A.

Revision History  

• Version 1.0: 2014-02-05
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description